Shallow coastal lagoons, especially the ones with clear waters and lighted substrata, are likely to have large microphytobenthos (MPB) communities. MPB is an important component of these systems, representing up to 99% of the chlorophyll concentration when compared to phytoplankton. It is therefore expected that MPB resuspension play a key role in the dynamics of phytoplankton due to the tide and wind action. Water samples were collected twice per month inside and outside Ria Formosa lagoon (Portugal), for nutrients and chlorophyll alpha (chl a). Sediment samples were also collected for MPB chl alpha. Chl alpha was also analysed in water and sediment samples from Venice lagoon (Italy), at least once per month. A truncated Fourier series was fitted to the data to investigate the seasonal and high-frequency components of the time-series. In the Ria Formosa, the best significant fit for MPB was obtained considering the sum of 26 wave-pairs (sin and cosine), which explained 31% of the variability. The seasonal cycle (1-3 waves) explained approximately 5% of the total variability. Within-day variability which includes spatial heterogeneity explained 61% of the variability. The best fit for phytoplankton inside Ria Formosa was obtained considering the sum of 23 wave-pairs. Outside the lagoon the best fit was obtained using only the sum of 16 wave-pairs. For both cases, the sum of waves explained more than 64% of the variability and the seasonal cycle explained more than 31% of the variability. It is expected that primary producers in the water column have a strong seasonal factor due to the direct effect of the solar cycle, which is the case of other clear waters. In the Venice lagoon, which is microtidal, the best fit for MPB was obtained using 10 wave-pairs. However, the best fit for phytoplankton was obtained with only 3 wave-pairs, indicating the importance of the seasonal cycle. Significant relationships were found between phytoplankton inside and outside the Ria Formosa, as well as between microphytobenthos and phytoplankton in the lagoons of Venice and Ria Formosa. These results suggest the influence of MPB resuspension in the phytoplankton community of shallow coastal lagoons and the importance of phytoplankton exportation to the coastal zone. (C) 2012 Elsevier Ltd. All rights reserved.