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Abstract The ability of fish to sustain environmental perturbations during fragile early‐life stages can be of vital importance for populations and species facing rapid global environmental change. One of the potential challenges for aquatic organisms, including teleost fish, is rising concentration of dissolved organic carbon (DOC) in freshwater environments, known as brownification, which causes a cascade of changes including a decreased visibility and pH. Conversely, humic substances are increasingly recognised for their potential antimicrobial and immunostimulant properties. The questions remain whether exposure to humic waters high in DOC during the development causes significant perturbation, and to what extent genetic and parental factors may maintain optimal development in such a possibly challenging environment. To address these questions, we generated pure and hybrid (inter‐population) crosses of Eurasian perch ( Perca fluviatilis ) originating from clear‐water and humic lakes. Fertilised eggs from each cross were exposed to natural humic and clear‐water lake water. Intra‐chorionic space diameter (embryo diameter) and hatching success were recorded. Perch embryos successfully developed even in a small volume of water (5 mL) and majority hatched (70%) by 13 day post‐fertilisation. Embryo diameter was influenced by the interaction between cross type and treatment where embryos with maternal clear‐water origin were smaller than embryos of humic water origin in both clear‐water and humic water treatments. The probability of hatching was not related to female size, but rather to embryo diameter at the eyed stage and the interaction between cross type and treatment, resulting in pure clear‐water crosses hatching earlier and at higher numbers. Our study shows that effects of humic water are not uniformally negative in perch and discloses population‐dependent responses to humic water exposure during development. Our experimental design also illustrates the utility of multi‐well plates for conducting complex high‐throughput experiments beyond traditional model species and opens new possibilities for testing perch genotype–environment associations in early‐life traits. Taken together, results of this study add to the growing evidence that humic substances may have complex effects on fish during early life, motivating further investigations on their role in shaping natural phenotypes and potential use in the applied sector.