Planktonic crustaceans are important part of carbon cycling in in shallow, temperate freshwater habitats. The objective of the study was to examine the link between selected environmental variables, densities of various groups of bacteria and δ<sup>13</sup>C of calanoid copepods, cyclopoid copepods and <em>Daphnia</em> sp. Generalized Linear Models (GLMs) with stepwise-selected environmental predictors showed that δ<sup>13</sup>C of calanoid copepods was positively correlated with the Day of the year and Other bacteria density and negatively correlated with NH₄⁺ and NO₃⁻ concentrations. Cyclopoid copepods’ δ<sup>13</sup>C was correlated exclusively with water temperature, which showed a positive effect on the stable carbon isotopes ratio. GLM for <em>Daphnia</em> sp. was the most complex and retained the Day of the year, Other bacteria density and PO<sub>4</sub><sup>3- </sup>as positively correlated predictors, while β-proteobacteria NH₄⁺ and NO₃⁻ were included in the model as negatively correlated predictors for δ<sup>13</sup>C. Our study highlights the complex impact of environmental conditions, microbial processes and functional trait-driven responses on δ<sup>13</sup>C values in planktonic crustaceans. Thanks to integration of plankton ecology, microbiology and the analysis of stable isotopes the study improves the understanding of carbon flow in shallow freshwater ecosystems.