Shallow lakes are frequently characterised by a consolidated sediment that is covered by an overlying floc layer. Arsenic and P remobilisation was related to differences in contaminant binding and sediment formation for two such sediments from Lake Yangebup, Western Australia. Chemical fractionation data, statistical relationships between total elemental concentrations, and mineralogy data highlighted differences in As and P binding in each sediment. The results showed that As and P are bound in a common Fe oxide fraction in the consolidated sediment, whereas in the floc As is mostly bound by adsorption and P is scavenged during Fe or natural organic matter sedimentation. The disparity between As and P binding in floc can be accounted for by differences in As and P oxidation state (As(III) v. P(V)), the incorporation of P but not As into natural organic matter, and the short time scale of floc formation. Arsenic and P behavior is closer in the consolidated sediment because As(III) gradually oxidizes to As(V) during consolidated sediment formation. The results demonstrate that, despite sediment heterogeneity and chemical complexity, contaminant binding and remobilisation mechanisms can be determined using a suite of simple chemical tests. This is important if remediation strategies are to be evaluated properly.