Attempts to control sediment-containing runoff and associated water quality problems have involved the establishment of many small to medium sediment retention ponds and the injection of nonionic and anionic polyacrylamide (PAM) flocculants to enhance colloid removal. However, to date use has been driven more by practicing engineers and trial-and-error approaches than by logical and consistent design approaches. Therefore, the purpose of this research was to optimize colloidal clay removal in PAM-aided sediment retention ponds by applying experimental and theoretical methodologies. Initially, simple measurement techniques for the molecular weight (MW) and charge density (CD) of various PAMs were tested and their characteristic behaviors in aqueous solution were investigated for use in subsequent optimization tasks. A simple intrinsic viscosity measurement technique and acid-base titration method showed their capabilities as the most plausible substitutes of state-of-the-art techniques in measuring MW and CD, respectively. Also, a cylindrical shape for PAM conformation in aqueous solution was shown to be the best assumption for predicting the characteristic behavior of PAM molecules. In adsorption and flocculation experiments with nonionic PAMs and negatively-charged kaolinite clay particles, adsorption capacities of PAMs on kaolinite were found to increase with increasing PAM MW up to a certain size (~ 18 M g/mol) but then decrease beyond this size due to entanglements between PAM molecules. Flocculation efficiency with nonionic PAM also increased with increasing MW up to a point due to its nonequilibrium kaolinite flocculation but eventually decreased by entanglements between PAM molecules. In parallel experiments with anionic PAMs and negatively-charged kaolinite particles, adsorption capacities were found to be inversely proportional to the PAM CDs, while flocculation efficiencies were directly proportional to the PAM MWs. Along with the effects of PAM MW and CD, the presence of divalent cations such as Ca2+ and Mg2+ enhanced adsorption and flocculation due to cationic bridging and/or charge screening between PAM and kaolinite (PAM-+M+-Kaolinite). However, concurring steric stabilization was also found to counteract flocculation due to the conformational compaction of adsorbed PAMs by the cationic bridging between pre-adsorbed PAM molecules (PAM-+M+-PAM). In short, PAM and solution characteristics, including change density (CD), molecular weight (MW) of PAM, and cationic species in the solution, were found to make critical effects on adsorption and flocculation and thus to be the controlling parameters in optimizing PAM applications as soil stabilizers or flocculants. In a model-based optimization of PAM-aided sediment retention ponds, the applicability of utilizing multi-dimensional Discretized Population Balance Equations combined with a Computational Fluid Dynamics (CFD-DPBE model) was demonstrated in a series of simulation tasks with a model retention pond. The CFD-DPBE model was demonstrated to be a valuable simulation tool for natural and engineering flocculation and sedimentation systems as well as flocculant-aided sediment retention ponds