Cyanobacterial blooms and their toxins are a major water quality and potential health risk around the world. This thesis developed an analytical method for microcystin congeners in sediments in order to examine their fate in lakes and establish the history of toxin-producing cyanobacteria in relation to environmental change using lake sediments. A novel method for both intra- and extracellular microcystins in lake sediments was developed, consisting of accelerated solvent extraction, hydrophilic-lipophilic balance solid phase extraction and multiple reaction monitoring-based HPLC-MS/MS quantitation. The method achieved comparable recoveries of intra- and extracellular cyanotoxins based on nine microcystins and nodularin (marine analogue). The analytical method was validated using surficial and deeper sediments from seven lakes of diverse geography and trophic state. To study the fate of microcystins, a multi-year, whole lake study of Microcystis blooms was conducted to obtain both in situ and in vitro half-life estimates of microcystin-LA (MC-LA), an understudied, but increasingly reported microcystin. MC-LA appeared to undergo slower rates of decomposition and persist longer than the more frequently studied MC-LR. Experimentally, high light intensity increased in vitro decomposition of dissolved MC-LA while high temperature enhanced decomposition in the particulate phase. Sediment deposition measurements and estimates of sediment-pore water distribution coefficients, sediment accumulation rates, and diffusive fluxes indicated that microcystin congeners differ in their fate. Notably, MC-LA preferentially distributed into pore water and remobilized (by diffusion) from sediments and into overlying water while MC-RR adsorbed more strongly to sediment particles. Finally, the sediment record of an eutrophic lake of major recreational importance was examined to identify possible drivers of toxigenic cyanobacteria and determine if the perceived increase in toxigenic cyanobacteria could be corroborated. Microcystins were detected to the bottom of the core (early 1800s), indicating that toxigenic cyanobacteria were present prior to the first permanent settlements. Microcystins were significantly correlated with changes in diatom-inferred nutrients (DI-TP and DI-TKN) within the sediment core as well as with specific algal pigments. Sediment microcystins in the upper layers also significantly correlated with a 20-year monitoring record for water column microcystins suggesting that sediment microcystins can be used as a proxy for past surface water conditions.