Fluid flow systems can include one or more thermoelectric devices in contact with the fluid flowing through the system. One or more thermoelectric devices can be operated in a temperature control modeand a measurement mode. Thermal behavior of the one or more thermoelectric devices can be analyzed to characterize a level of deposit formed on the thermoelectric device(s) from the fluid flowing through the system. Characterizations of deposition on thermoelectric devices operated at different temperatures can be used to establish a temperature-dependent deposition profile. The deposition profile can be used to determine if depositions are likely to form at various locations in the system, such as at a use device or in a flow vessel. Detected deposit conditions can initiate one or more corrective actions that can be taken to remove deposits, or to prevent or minimize deposit formation before deposits negatively impact operation of the system.