1. Repeat sampling in daytime within a lily (Nuphar lutea) bed and in open water showed distinct heterogeneities in the three-dimensional distributions of water chemistry and planktonic organisms on centimetre to decimetre scales.
2. Vertical gradients of physico-chemical variables that did not exist at dawn developed during the day in both sites, as available nutrients were released from the sediments and were consumed towards the surface.
3. Distributions of algal standing crop suggest limitation by both nutrients and grazing.
4. Marked variability in distributions may question the assumptions often made about the homogeneity of plankton and available nutrient distributions in open water and in macrophyte stands of shallow lakes. Although simple sampling regimes for monitoring of water quality may be adequate for many purposes, they miss a fine structure in the water that is inherently interesting in understanding the underlying processes of plankton function.