There are several methods for measuring flow rate for a potential micro-hydro scheme. The methods vary in both complexity and accuracy.
There is some initial advice below. We can offer a detailed assessment through CAT Consultancy.
For a small stream, the easiest way is to divert the entire flow into a container of known size and time how long it takes to fill. Dividing volume by time will give an rough estimate of the flow rate.
For a larger stream, an initial estimate can be made by multiplying the speed of the water by the cross-sectional area. The speed is measured by timing a float along a measured distance of stream (preferably straight and free from obstacles) and multiplying by a factor of between 0.8 (straight smooth channel) and 0.6 (rocky stream). The area can be calculated by measuring the depth at several points across the stream, taking the average and multiplying by the width at that point.
A more accurate method of flow measurement involves building a wooden weir across the stream, with either a V-shaped or rectangular notch cut in it. If the height of water flowing over the weir is measured, then the flow rate can be worked out (see below). Although this method involves a lot of work initially, it is then easy to take readings from the weir over a period of time and establish the flow variation.
An entirely different approach is to calculate the catchment area of the stream from a large scale map and then calculate the expected run-off using rainfall statistics such as those available from the Met Office (http://www.metoffice.gov.uk/climate/uk/summaries). You'll need data about geology, rainfall, transpiration and evaporation. Results from this method can be extremely accurate, and they also predict how the flow will vary over the year.
Another option is 'salt gulp': add salt solution and measure conductivity downstream with conductivity meter. This is only worth buying if doing a lot of site assessments, as it costs a few hundred pounds.
Notched weirs for assessing river / water flow:
Please Note: you'll need to use either a computer spreadsheet or scientific calculator to calculate these equations, because of the exponential functions.
For a v-notch (90 degrees) weir: Q = 1.4 x h^2.5 (i.e. h to the power of 2.5, then multiplied by 1.4)
For a rectangular weir: Q = 1.8 x ( L - 0.2 x h ) x h^1.5
Q is the flow rate in cubic metres per second
h (in metres) is the height of water above the base of the notch
L is the width of the rectangular notch, and must be at least 3 x h.
The distance from the outer edge of the notch to the stream edge/bank should be at least 2 x h (for both types of weir)
The weirs need to be watertight, with accurate angles and sharp edges, and be mounted vertically and at right-angles to the water flow. The weir should be ventilated by air under the crest of falling water. A 'stilling pond' just upstream will help to keep the velocity of water before the weir to no more than 0.2 metres per second.
There is much greater detail about these methods and other ways of measuring flows, catchment areas, etc, in the book 'Going with the Flow' (by Langley & Curtis). Unfortunately this book is currently out of print, but you may be able to find it through a library or second-hand.