NIWA has built flow stations on rivers and canals for decades. While technology has changed over the years, we've still achieved a high level of standardization.
Because continuous direct water flow measurement can be complicated and time consuming, the standard method that NIWA uses in its National Hydrometric Network and Irrigation Scheme water flow stations is to measure water level, which is comparatively easy, and calculate the flow from a mathematical equation.
We can get this equation two ways:
We can build a "v notch' weir at the site and measure water level upstream of it. The geometry of the weir defines the mathematical relationship. The weir is usually made from concrete and so the equation stays accurate for the life of the weir.
We can choose a stable site and carry out a gauging to establish the relationship between water level and flow rate. The relationship may need to be re-established regularly, but this depends on the stability of the channel cross section.
NIWA's standard method is to measure water level using a stilling well and water level encoder connected to a recording device.