Day and nighttime autumn fish abundance and biomass were studied in the pelagic and littoral zones of Lake Sauka in Latvia. Both pelagic methods (hydroacoustics and trawling) revealed significantly higher fish abundance and biomass during the day than at night, especially in deeper zones (below 3 m). Roach (Rutilus rutilus) and Eurasian perch (Perca fluviatilis) dominated the trawl catches during the day, while roach and ruffe dominated at night. Fish smaller than 14 cm strongly dominated in both the trawl catches and hydroacoustic observations. Our hydroacoustic sampling found inhomogeneous pelagic distributions of fish aggregated in big shoals during the day. In the littoral zone, which was sampled by beach seining, both the abundance and biomass were significantly higher at night than during the day. Roach, bleak, and European perch usually dominated in beach seine catches during the day and at night. The daytime pelagic biomass found by hydroacoustics was 62 kg/ha and it decreased to approximately 11 kg/ha at night. The littoral biomass found by beach seining was diurnally opposite, 4 kg/ha during the day and 37 kg/ha at night. It is obvious that diurnal horizontal migrations between pelagic and littoral zones, and shoaling behavior during the daytime are common patterns in the shallow Lake Sauka during the autumn. The study of the spatial distribution of fish is extremely important for the establishment of an appropriate monitoring plan for the purposes of the Water Framework Directive with regard to the morphometry of the lake, the geographical location, and the sampling period of the year. This study also shows that the combination of completely non-invasive hydroacoustic and other methods that are invasive (trawls, beach seines) but not as destructive as gillnets, which are normally used for scientific fish monitoring in Europe, could be a future way forward for fish monitoring.