Evaluating sediment recontamination due to storm water discharges is important when evaluating the long-term effectiveness of sediment remediation efforts at reducing biological impacts. The bioaccumulation of the heavy metals zinc, nickel, copper, cadmium, mercury, and lead and the metalloid arsenic in a clam (Macoma nasuta) was studied in surficial sediments before and after storm water inputs from Paleta Creek, California, USA, during wet seasons in 2015 to 2016 and 2016 to 2017. The bioaccumulation was compared with bulk sediment concentrations and porewater concentrations measured by diffusion gradient in thin film devices. Significant reductions in biota accumulation and porewater concentrations were observed in samples collected after storm seasons compared with before storm seasons despite bulk sediment concentrations remaining the same or increasing. This was apparently the result of the deposition of storm water contaminants in low bioavailable forms. The bioaccumulation of all the measured contaminants showed a positive significant correlation with porewater concentrations (p < 0.1, α = 0.1) and weak or no correlations with bulk sediment concentration. In conclusion, observed bulk sediment recontamination due to storm water should not be assumed to lead directly to greater biota accumulation without bioavailability assessment.