Benthic, pelagic and littoral-habitats are linked by physical processes in lakes. Exchanges between littoral and pelagic regions or between sheltered embayments and open waters can occur when horizontal density differences are generated. The resulting flows have been observed in tropical, subtropical, and temperate lakes as a result of differences in rates of heating due to morphometry or variations in algal abundance and differences in the depths of wind mixing. Laboratory experiments show that such circulations can also occur under beds of floating vegetation These circulations may be significant for the movement of nutrients within lakes. Whereas mixing induced by wind is often invoked as a mechanism for vertical transport, the depth of penetration of wind-induced mixing may be suppressed if rates of heating are high when wind speeds are high. Consequently, if nocturnal heat losses are high, the convective motions induced by thermal instabilities may be more important than wind mixing for ventilation of deep water with its typically higher concentrations of nutrients and dissolved gases. Even when mixing in shallow waters is induced by wind and by shear instabilities in the diurnal thermocline, mixing may be incomplete when stratification induced by diurnal heating is strong; gradients in nutrient concentrations and in phytoplankton distributions may persist. Resuspension of living and non-living particles from the benthos can reseed phytoplankton to the upper layers and alter rates of nutrient supply or scavenging of pollutants. Resuspension tends to be higher in shallow waters; subsequent horizontal transports convey these materials to the pelagic zone. Assessing the time and space scales for physical, chemical and biological processes facilitates the design of studies to show the coupling of these processes.