Juvenile mussels enter the benthos after excysting from a fish host and settling to the bottom where they inhabit the interstitial zone in rivers.  We examined the algal composition in the surface water and pore waters in different locations in a temperate river (Thames River) in Southern Ontario.  Surprisingly, algal concentration (C) was ~9× higher in pore water versus surface water, varied spatially in the riverbed (downstream of boulders > upstream of boulders and non-bedform regions), and pennate diatoms were the most abundant taxon in the pore waters.  We examined the clearance rate (CR; mass of suspended material removed from the water per unit time and mussel) of recently metamorphosed juvenile unionid mussels (3 – 4 week old Lampsilis siliquoidea, Fatmuckets) exposed to pore water and surface water in a paddle-wheel flow chamber at different water velocities (U).  Juvenile CR based on chlorophyll a fluorescence was ~2× higher on pore water versus surface water and CR based on a specific algal taxon, identified via flow cytometry, varied with its initial concentration.  Chesson’s feeding electivity index revealed that mussels removed 5 chlorophyte taxa in proportion to their concentration in the water (i.e., removed at random) but they removed 5 diatom taxa in greater proportion (i.e., selected for by juvenile mussels) across the range of algal flux (J = UC) examined.  This study provides evidence of the importance of diatoms in pore waters to juvenile mussels.  It also reveals elements of the physico-chemical environment used by juvenile mussels, which should be considered in their conservation.