The effect of catchment nutrient inputs in stimulating primary production in nutrient depauperate freshwater systems is well documented globally. However, assessing the relative effect of different soil and terrestrial plant litter, and it’s associated nutrients and organic carbon, on phytoplankton productivity is challenging. Our research is combining chemical measures with phytoplankton bioassays as a means of comparing an ecosystem response to catchment drivers of productivity. We have also used bioassays to examine phytoplankton responses to sediment derived from a range of soil types. Sediment nutrient can become rapidly bioavailable to phytoplankton, eliciting growth-related responses, with different soil types differentially affecting phytoplankton responses, which has important management implications. Leaf litter can also contribute complex organic compounds to waterways, which our studies have shown can have both negative and positive effects on phytoplankton. Our understanding of the complexity of phytoplankton responses to catchment inputs is still largely focussed on inorganic nutrients, however it is clear that responses to catchment inputs of nutrients and organic carbon are far more complex than previously thought. This information is critical to informed management and remediation of catchments for beneficial water quality outcomes.