The densely populated North Sea region encompasses catchments of rivers such as Scheldt and Meuse. Herein, agricultural, industrial, and household chemicals are emitted, transported by water, and deposited in sediments, posing ecological risks. Though sediment monitoring is often costly and time-intensive, modeling its toxicity to biota has received little attention. Due to high complexity of interacting variables that induce overall toxicity, monitoring data only sporadically validates current models. Via a range of concepts, we related bio-physicochemical constituents of sediment in Flanders to results from toxicity bioassays performed on the ostracod Heterocypris incongruens. Depending on the water body, we explain up to 90% of the variance in H. incongruens growth. Though variable across Flanders' main water bodies, organotin cations and ammonia dominate the observed toxicity according to toxic unit (TU) assessments. Approximately 10% relates to testing conditions/setups, species variabilities, incoherently documented pollutant concentrations, and/or bio-physicochemical sediment properties. We elucidated the influence of organotin cations and ammonia relative to other metal(oxides) and biocides. Surprisingly, the tributylin cation appeared ∼1000 times more toxic to H. incongruens as compared to "single-substance" bioassays for similar species. We inferred indirect mixture effects between organotin, ammonia, and phosphate. Via chemical speciation calculations, we observed strong physicochemical and biological interactions between phosphate and organotin cations. These interactions enhance bioconcentration and explain the elevated toxicity of organotin cations. Our study aids water managers and policy makers to interpret monitoring data on a mechanistic basis. As sampled sediments differ, future modeling requires more emphasis on characterizing and parametrizing the interactions between bioassay constituents. We envision that this will aid in bridging the gap between testing in the laboratory and field observations.