Stream-bed life as indicators of stream health

The plants and animals that live on the beds of streams can provide a very good indication of overall stream health.

This is because many organisms have preferences for certain ranges of conditions.

Stream-bed organisms making up a community are an “integration” of the physical and chemical state of the stream over, say, a week or two. This contrasts with direct measurement of chemical composition of the water. The latter provides only a brief “snapshot” of stream quality. For this reason, biological monitoring has become very widespread in scientific monitoring programmes both in New Zealand and overseas.

The biological monitoring system in SHMAK is based on methods currently in use in New Zealand.


Invertebrates, literally, are “animals without backbones”. They include, for example, the arthropods [animals with jointed legs and exo-skeletons (outside skeletons), e.g., insects, crustaceans, spiders]; molluscs [animals with shells, e.g., snails, bivalves (mussels)]; and a variety of different worm-like creatures. Of those insects that inhabit streams, many are the juvenile (or larval) forms.

Most invertebrates are quite small; indeed many are practically invisible to the naked eye. For the stream-bed survey, we concentrate on the “macro-invertebrates”, which are clearly visible to the naked eye. Use of a hand lens which magnifies just two to three times makes examination of invertebrates much easier.

Rather than try to identify all invertebrates found on the stream bed, we have selected a set of 17 types or taxa. Together these can give us a good idea of stream health for the following reasons.

  • Each type (or taxon) is tolerant of a different range of physical and chemical stream conditions. A score has been assigned to each taxon according to where the tolerance range lies in the spectrum from a really healthy stream to a very degraded one. The scores range from 1 to 10 and most are based on the Macroinvertebrate Community Index (MCI) which was originally worked out for invertebrates in the Taranaki region (Stark 1985).
  • They are relatively easy to recognise by non-experts with a little training.
  • They are easy to collect.
  • Invertebrates in general are good “integrators” of stream condition at a particular site because most do not move around very much in the stream. The community is therefore susceptible to the effects of localised pollution and disturbances.
  • The 17 categories alone should give a good idea of stream condition and there is no need to take any other invertebrate types into account.

Notes follow on each of the 17 “indicator” taxa (types).


Description on form: Worms (thin brown/red)

Score: 1 [worms (thin brown/red)].

Scientific name(s): Oligochaetes, various species.

Range of sizes: 2–6 cm long, about 1-3 mm diameter.

Features to look for: Range of features from thread-like worms, white, red or brownish in colour to more traditional ‘earthworm’ like features.

Where: Often in mud or silt in degraded lowland streams; sometimes in great numbers. Can be found in small numbers in most stream types. Don’t confuse them with “bloodworms” (chironomid larvae) which are shorter, brighter red and with a distinct head and eyespots.


Description on form: Flatworms

Score: 3 [flatworms, leeches].

Scientific name(s): Platyhelminthes.

Range of sizes: up to 1 cm.

Features to look for: Small, brownish, undefined shape; they move with a creeping motion (see photo).

Where: Better known as internal parasites, the Platyhelminthes also have freshwater species. Flatworms are fairly tolerant but occasionally turn up in quite clean waters as well. High mountain streams often have good numbers of flatworms.


Description on form: Freshwater crustaceans (amphipods, water fleas)

Score: 5 [freshwater crustaceans].

Scientific name(s): Crustacean orders Amphipoda and Cladocera.

Range of sizes: 1–10 mm long.

Features to look for: Amphipods are up to 10 mm long, but are usually a lot smaller, and look like tiny shrimps,. Colouration ranges from very dark to very pale. Water fleas are tiny, grey-brown flea-shaped creatures; very active and often in great numbers. The legs are clearly visible (especially if you use a hand lens to look at them.) Where: At the margins of slow-flowing streams, particularly amongst submerged weed beds.


Description on form: Small bivalves

Score: 3 [small bivalves].

Scientific name(s): for exae, Pisidium sp.

Range of sizes: 2–4 mm wide.

Features to look for: Tiny, grey-brown or whitish double shells, like miniature mussels or clams.

Where: At the margins of silty, slow-flowing streams.


Description on form: Snails, rounded

Score: 3 [snails, rounded].

Scientific name(s): Physa and others.

Common name(s): Water snails.

Range of sizes: Usually 4–6 mm across.

Features to look for: Again clearly snail-like; colour from light beige to darker brown, with markings. The shell is quite rounded with the top of the spiral a small peak. You’ll sometimes see clear, jelly-like blobs of snail eggs in the same areas.

Where: Mainly found in enriched (degraded?) water, on upper and undersides of stones. Physa is an introduced snail capable of living in stagnant conditions because it can ‘breathe’ air, unlike many other snails that rely on dissolved oxygen.


Description on form: Snails (pointed end)

Score: 4 [snails (pointed end).

Scientific name(s): Potamopyrgus.

Common name(s): Water snails.

Range of sizes: Typically 1–4 mm across.

Features to look for: Obviously snail-like, but tiny and often almost black; sometimes lighter brown. The top of the spiral is pointed.

Where: Found in range of stream types, usually most abundant where the water is quite enriched. Often on the undersides of stones, also on water plants and among algae. Potamopyrgus is sometimes extremely abundant.


Description on form: Limpet-like molluscs

Score: 7 [limpet-like molluscs].

Scientific name(s): Latia sp. (pictured); Ferrissia spp.

Range of sizes: 2–8 mm wide.

Features to look for: Dark coloured shells adhering to rocks. When empty, the shells appear a lighter russet-brown colour. Often very abundant. Where: Latia is restricted to the North Island, whereas Ferrissia can be found on both main islands. Latia prefers larger stones in relatively stable streams. Ferrissia is often abundant on aquatic plants.


Description on form: “Axehead” caddis larvae

Score: 3 ["axehead" caddis larvae].

Scientific name(s): Oxyethira albiceps (1); Paroxyethira sp. (2)

Range of sizes: Up to 3 mm long.

Features to look for: A tiny cased caddis larva with a wedge-shaped case, something like an axehead (sometimes also called purse-cased caddis). The pupae are a similar shape and are firmly attached to rocks.

Where: Axehead caddis larvae are found attached to stones or other substrate in streams with slow-flowing, relatively enriched water; or among periphyton growth, which they feed on. Because of its tolerance to enriched waters, Oxyethira is in a category separate from other caddisfly larvae.


Description on form: Midge larvae

Score: 2 [midge larvae].

Scientific name(s): Chironomidae (family).

Range of sizes: 2–5 mm long, very slender.

Features to look for: Tiny, white, brownish, bright red or transparent wriggling worm-like larvae. Have a distinct head and eyespots. Body diameter more or less uniform. Red chironomids (“bloodworms”) can be distinguished from worms by their movement, their brighter red colour, and their legs.

Where: Often in large numbers on the tops of rocks Associated with algal mates, but are also often abundant on submerged plants and in silt/mud on the streambed. Not always noticeable straight away: but scrape off the algae you should see them move using a looping motion. Red chironomids (“bloodworms”) occur in silt.


Description on form: Damselfly larvae

Score: 4 [damselfly larvae].

Scientific name(s): Odonata (Zygoptera) (e.g., Xanthocnemis).

Range of sizes: 1-2 cm long.

Features to look for: Sandy-coloured, delicate larvae, with leaf-like gills that look like tails. Unlike the mayflies (which also have three tail filaments) damselfly larvae do not have gills along the sides of the body.

Where: In slow-flowing streams, often associated with aquatic plants.


Description on form: Cranefly larvae

Score: 5 [cranefly larvae].

Scientific name(s): e.g., Aphrophila sp.

Range of sizes: up to 2.5 cm.

Features to look for: Cranefly larvae are fat grayish-brown or light green grubs. The head is retracted into the body so is not obvious. The body is segmented and may have “false legs” that look like ridges visible on the body between each segment.

Where: Cranefly larvae are moderately tolerant and are found in stony streams of varying quality.


Description on form: Beetle larvae and adults

Score: 6 [beetle larvae and adults].

Scientific name(s): e.g., Elmidae.

Common name: Riffle beetles.

Range of sizes: Adults 2-3 mm long , larvae up to 7 mm long.

Features to look for: Small black beetles present only in summer. The larvae look a bit like some chironomids; but they look “striped”, have well-defined jointed legs, and have a more crawling type of movement (as opposed to the wriggling of chironomids).

Where: Adults clinging to the underside of rocks in faster-flowing water; larvae on top of stones, often abundant in runs in gravel bed streams.


Description on form: Caddisfly larvae (rough, stony cases; free-living)

Score: 6 [caddisfly larvae (several types in this category)].

Scientific name(s): Trichoptera (family); various taxa.

Range of sizes: Up to 2 cm long.

Features to look for: Many caddis larvae build cases in which they live, made of small stones, sand grains, even twigs and pieces of leaf. Some move around taking their cases with them. Others are free living, but may build “houses” of small stones to which they can retreat. The next three descriptions illustrate common types of caddisfly larvae. For SHMAK, they are all counted in a single category of invertebrate.

Where: These types of caddis are found in a range of water and stream types in moderate-to-fast flowing water, amongst or on stony substrates. Several species are also found in lowland, soft-bottomed streams, and often form one of the more sensitive groups in these habitats.


Common name: Common stony-cased caddis

Score: 6 [caddisfly larvae (several types in this category)].

Scientific name: e.g., Pycnocentria sp. (pictured).

Range of sizes: <10 mm (length of case).

Features to look for: A caddis which moves around carrying its case. The case is a slightly curved cylinder tapering towards one end. It is made of tiny stones or particles of sand and is dull brown in colour.

Very common in stony streams in a range of water types.


Common name: Free-living caddis larvae (stony houses)

Score: 6 [caddisfly larvae (several types in this category)].

Scientific name(s): e.g., Aoteapsyche sp.

Range of sizes: Up to 2 cm long.

Features to look for: A free-living caddis which builds itself a stony retreat for pupation. You’ll notice the stone “houses”. The larva itself has a brown head, brown plates on the upper side behind the head and short legs. The rest of the body is fat, light brown and grub-like, with gill-tufts on its underside.


Common name: Green caddis (another free-living caddis larva)

Score: 6 [caddisfly larvae (several types in this category)].

Scientific name(s): e.g., Hydrobiosis sp.Range of sizes: Up to 2 cm long.

Features to look for: A free-living, predatory caddis larva which builds a stony house only when it is about to pupate (transform into an adult). Dark, flattened, head; pincer-like front legs; slender, bright green, grub-like body. Often very aggressive when captured. There are also brown-coloured taxa (as pictured).


Common name: Smooth-cased caddisfly larvae


Score: 9 [smooth-cased caddis larve].

Scientific name(s): Olinga feredayi, Beraeoptera.

Range of sizes: Up to 10 mm long (with case).

Features to look for: Olinga and Beraeoptera are smooth-cased caddis. The case is a distinctive chestnutcolour, without stones/sticks or other material stuck to it. It is usually not as common as the stony-cased caddis.

Where: Mostly in clean streams, under stones. Smooth-cased caddis are treated as a separate category because of its preference for cool, clean, stony streams.


Common name: Spiral caddis

Score: 10 [spiral caddis].

Scientific name(s): Helicopsyche sp.

Range of sizes: Up to 3 mm across (with case).

Features to look for: A cased caddis with a flattened spiral house made of sand grains and fine grit; light brown in colour. Can be very common.

Don’t confuse these with snails! Look for the gritty appearance of the case, compared with the smooth shell of snails.

Where: These caddisfly larvae occur only in really clean streams, hence their high score. Again they are treated in a separate category.


Description on form: Mayfly larvae

Score: 9 [mayfly larvae].

Scientific name(s): e.g. Deleatidium sp.

Range of sizes: Body up to 2 cm long.

Features to look for: Mayflies make quick, distinctive movements – they seem to undulate side-to-side. Even very tiny ones can be picked out from this. They have three long tail filaments and well-developed legs.

Where: Almost always found on the underside of stones, in clean water. In the North Island mayflies are also found associated with submerged aquatic plants in cool, clean streams. Mayflies are an important part of fish diets in some streams because they drift in the currents where trout can easily prey on them. (Fly fishermen try and imitate these mayflies.)


Description on form: Stonefly larvae

Score: 10 [stonefly larvae]. 

Scientific name(s): e.g. Stenoperla, Austroperla (pictured).

Range of sizes: Up to 2.5 cm long.

Features to look for: Stonefly larvae have two “tail filaments” and long antennae. The legs are prominent and stick out like elbows. S. prasina has a distinctive green body, with an orange underside. Austroperla has three thin gill filaments coming out from between its two more robust tail filaments.

Where: Stonefly larvae are found in cool, clean, stony streams.


Not an “indicator”, but worth mentioning: Sandfly larvae

Score: don't score these! [sandfly larvae].

Scientific name(s): Austrosimulium sp.

Range of sizes: 2–5 mm long.

Features to look for: These are small larvae, fatter than chironomids, with a characteristic bottle-shaped base; attached to rocks. You may also see pupae (resting stage) of sandflies: about 2–3 mm across, shield-shaped, with a pair of protrusions at the top. Of course the adults need no introduction to most outdoors lovers in New Zealand.

Where: You are bound to come across these at some stage. They have not been included in this assessment because these rather tolerant insect larvae are widespread in many streams, from pristine forest streams to impacted lowland waterways. Therefore they are not particularly good “indicators”.


Understanding your invertebrate scores: summary

Score: 0 to 1.9

The invertebrates at this site are only (or mainly) robust types. This would usually indicate polluted waters, particularly if water clarity is low and conductivity is high. If the stream bed is composed of gravels or cobbles, then the presence only of organisms that have scores of 0 to 2 usually indicates very degraded water quality.

Score: 2 to 3.9

The invertebrates at this site are robust or moderately robust types. This could indicate polluted waters if the stream bed is composed of gravels or cobbles. However, if the stream bed is naturally composed of sand/silt, slow flowing waters (e.g. < 0.1 m/s velocity) and/or large submerged plants then this is the natural habitat for many of these organisms and the degree of water quality degradation should also be inferred from water clarity, conductivity and pH.

Score: 4 to 5.9

Most invertebrates at this site are fairly robust types. These could indicate slightly to moderately polluted waters if the stream bed is composed of gravels or cobbles. However, if the stream bed is naturally composed of sand/silt or bedrock, the flow is naturally slow (e.g., velocities of less than 0.1 m/s) and there are large submerged plants then this is the natural habitat for many of these organisms and the degree of water pollution may be low. The water clarity results will provide a useful assessment of degradation from suspended silts, etc. and the conductivity results will assist with determining the degree of enrichment.

Score: 6 to 7.9

Most invertebrates at this site are not robust to degraded water quality and therefore suggest that you have a moderately healthy stream.

Score: 8 to 10

The invertebrates at your site are all sensitive to degraded water quality so this suggests that your stream is healthy. If only mayflies are found in your samples it may also indicate an unstable gravel bottom and/or that a flood has occurred recently. (Many gravel bed rivers of the South Island are dominated by the mayfly Deleatidium).



Periphyton is the slimy stuff you see growing on stream-bed rocks and stones, or sometimes as a film or filaments on a stable sandy bottom. It ranges in colour and form from bright green “clouds” of filaments to thin yellowish-brown slimy films to shiny black or brown-whitish “mats”. Literally periphyton means “around plants”, implying that it grows closely attached to a substrate. The term covers mostly algae, though small amounts of bacteria and fungi may be included in the slime. This community is a very important component of the stream ecosystem as it is more or less the bottom of the food chain. A range of invertebrates “graze” periphyton as their main food source.

Like macroinvertebrates, the periphyton community is a very useful indicator of the overall condition of a stream.

  • Periphyton does not move around at all, therefore it is a good integrator and indicator of local pollution and disturbance, even when the pollution can no longer be detected in the water by most chemical analyses.
  • Periphyton is easy to collect and relatively easy to assign to indicator categories.

A rough quantitative measure has been included in the list of periphyton indicator types, viz., a thin film; a medium mat; a thick mat; short filaments; long filaments. The thickness/length of periphyton growth depends on several factors:

  • the amount of nutrients in the water (enrichment);
  • the length of time the periphyton has been growing (since the last flood washed away growth);
  • the amount of invertebrate grazing.

Studies have shown that the most important of these factors is the length of time since the last flood. This highlights the importance of not assessing periphyton growth immediately following a flood (say, within 2 to 6 weeks, depending on location in New Zealand) or after a very long period of low flows (say, more than 12 weeks). In the former case, much of the periphyton crop will have been washed away; in the latter, growth may well be thick and patchy because low, slow flows have allowed more growth to accumulate than usual. In both these cases, periphyton growth is not “typical”.

Periphyton usually consists of a diverse mixture of algae. Experienced biologists may be able to identify some filamentous species from their macroscopic appearance, but normally a microscope is needed for identification. In general colour and texture provide some clues to the algal groups present. For example, a thin green film is likely to comprise some kind of colonial green alga. Brown films and mats of all thicknesses are almost always mainly diatoms – single-celled algae characterised by their silica “skeletons” (the feature usually used in species identification) and yellow-brown pigments (hence the brown colour). Patchy brownish blobs may be red algae. Green tufts and strands are filamentous green algae. Brown trailing filaments may indicate some filamentous forms of diatom, or they may be another algal group, the yellow-green algae. Sometimes, green algae look brown if they become coated with diatoms growing on the outer cell wall as epiphytes. Medium or thick dark shiny mats (listed as “black”) are usually blue-green (i.e., cyanobacterial) filaments.

The indicator groups listed on the periphyton monitoring form cover most categories of periphyton normally found in New Zealand streams. Scores are assigned according to the conditions in which each category is usually found growing dominating the cover of stream beds.


No periphyton

Score: no score.

Sometimes streams have no visible periphyton growth. Stones do not feel at all slimy or slippery to touch and no colour comes out with firm brushing with a toothbrush. There are two main reasons for this. First, invertebrates may be grazing the algae as fast as it is growing. Second, a recent high flow could have scoured away all growth. No periphyton survey is possible. For the second case, it is likely that there will be few invertebrates present too, and it may be better to postpone the monitoring. (See pages 9.1–9.2 for notes about the effects of high flows on stream ecosystems.)


Thin mat/film (less than 0.5 mm thick)


Score: 7 [thin green film]. 

A very thin green film indicates growth of encrusting single-celled green algae, which indicate slightly enriched conditions.

Light brown:


Score: 10 [thin light brown film].

A thin yellowish-brown or reddish-brown sheen on rocks almost always consists of diatoms. These are single-celled algae which have silicon (glass) cell-walls, and brownish cell pigments. In clean water with low nutrient concentrations, the layer will remain thin, particularly since invertebrates will graze on it.

Black/dark brown:


Score: 10 [thin black/dark brown film].

Very dark thin coatings on stones usually contain some blue-green algae as well as diatoms. In clean waters, the layer will often remain thin.


Medium mat or film (0.5 to 3 mm thick)


Score: 5 [medium green mat].

Thicker encrusting green algae indicate prolonged moderate to high nutrient conditions. A mixture of very short filamentous and other algae can have the appearance of a mat.

Light brown:

Score: 7 [medium light brown mat].

Thicker mats of diatoms will develop in slow-flowing waters with moderate enrichment

Black/dark brown:

Score: 9 [medium black/dark brown mat].

In slow-flowing water, moderately thick patches of blue-green algae can develop, even if the water is extremely clean.


Thick mat (over 3 mm thick)


Score: 5 [thick green mat].

Heavy growth of green algae is normally formed from the filamentous types. The thick mats of coarse green algae shown are Vaucheria, which develops in sluggish flows and often fairly enriched nutrient concentrations.

Light brown:

Score: 4 [thick light brown mat].

Thick, slimy (or “jelly-like”) masses of diatoms will form on the tops of rocks after prolonged sluggish flows and moderate to high nutrient concentrations. The diatoms are usually types that have stalks to attach them to the stones. These growths may appear more whitish than brown under certain conditions (particularly after long periods of stable flow).

Black/dark brown:

Score: 7 [thick black/dark brown mat].

These are predominantly blue-green algae. Thick growths can occur even in quite low-conductivity water. The “solid” brownish growths that grow in low nutrient concentrations during long stable periods are blue green algae (Nostoc). The latter is very common in Otago.


Filaments, short (less than 2 cm long)


Score: 5 [short green filaments].

Filamentous green algae normally grow best in moderate to high conductivity, slow-flowing water. Patches of short filaments often occur amongst moderately thick diatom growth.


Score: 5 [short brown/red filaments].

Some kinds of diatoms grow in filaments if the flow is slow enough.


Filaments, long (more than 2 cm long)


Score: 1 [long green filaments].

Long green filaments almost always indicate high-nutrient conditions and prolonged slow flows. In extreme cases, the filaments can cover the entire stream bed. Such heavy grows have detrimental effects on the stream for other stream life For example, wide daily swings in pH may result (see pages 9.4–9.5).


Score: 4 [long brown/red filaments].

Again, long brown filaments consist of diatoms. Coarse, dull-brown filaments could also be green algae covered with a thin growth of small, attached diatoms.


Understanding your periphyton scores: summary

Score: 0 to 1.9

There are mainly long filamentous green algae at the site indicating that there is moderate to high enrichment from phosphorus and/or nitrogen. Such enrichment could be from enriched seepage, a discharge from a treatment pond or could occur naturally in streams that have a high proportion of mudstone/siltstone or recent volcanic rocks (central North Island) in their catchments.

Score: 2 to 3.9

These communities suggest a moderate level of enrichment from phosphorus and/or nitrogen. Such enrichment could be from enriched seepage, a discharge from a treatment pond or could occur naturally in streams that have a high proportion of mudstone/siltstone or recent volcanic rocks (central North Island) in their catchments.

Score: 4 to 5.9

These communities suggest slight enrichment from phosphorus and/or nitrogen. Such enrichment could be from enriched seepage, a discharge from a treatment pond or could occur naturally in streams that have a high proportion of mudstone/siltstone, recent volcanic rocks (central North Island), limestone or marble in their catchments. Clean stones can result from recent abrasion by flood flows or intense grazing by invertebrates/insects that live in the gravels.

Score: 6 to 7.9

These communities are generally composed of species that are able to grow under moderate to low nutrient conditions. These communities also usually grow back first after a flood has removed previous growths, but may be out-grown by filamentous algae if nutrient levels are sufficiently high.

Score: 8 to 10

These communities usually signify low concentrations of nutrients and/or intensive grazing by invertebrates/insects that live among the gravels.