Resin and fatty acids (RFA) are predominantly components of coniferous trees having the natural function of protecting against microbial damage. These compounds are released from wood during the pulping process and a fraction reaches the wastewater treatment system. RFA are acutely toxic to aquatic organisms at concentrations on the order of parts per million, and their presence has been linked to toxicity outbreaks in receiving waters following process upsets. The chronic toxicity of resin and fatty acids in complex effluent matrices is poorly understood. Furthermore, the role of hydrophobic, pulp-derived solids as a removal pathway from wastewater streams has not been comprehensively studied. The objectives of this dissertation have been to quantify the relationship between resin and fatty acid concentration and chronic toxicity and to determine the role of partitioning in the removal of these compounds from pulp mill wastewater streams. Field and laboratory studies were conducted to measure toxicity using the Microtox™ whole effluent toxicity and Ceriodaphnia dubia 7-day, survival and reproduction bioassays. One resin acid in particular, dehydroabietic acid, was found to account for a significant fraction of final effluent chronic toxicity. Dissolved and sorbed RFA concentrations were quantified by solvent extraction, methyl ester derivatization, and GC-FID analysis. Partitioning to suspended solids was found to be a major removal pathway for the RFA from the effluent treatment system. A kinetic model for flotation was applied and compared to experimental data. Flotation was found to be effective at selectively removing RFA bound to pulp-derived solids from pulp mill and bleach plant sewers at moderate to high pH.