The interaction between physical and biological factors responsible for the cessation of ripple migration on a sandy intertidal flat was examined during a microalgal bloom period in late winter/early spring, as part of a wider study into the biostabilisation of intertidal sediments. Ripple positions and ripple geometry were monitored, and surface sediment was sampled, at weekly intervals over a 5-week period. Ripples remained in the same position for at least 4 weeks, during which time there was a progressive reduction in bedform height (smoothing) and deposition of some 1.5 cm sediment, mainly in the ripple troughs (surface levelling). The mean chlorophyll a (chl a) sediment content was 6.0 µg gDW−1 (DW: dry weight) (0–1 mm depth fraction), with a maximum value of 7.4 µg gDW−1 half way through the bloom. Mean colloidal-S carbohydrate (S: saline extraction) content was 131 µg GE gDW−1 (GE: glucose equivalent) (0–1 mm), with a maximum of 261 µg GE gDW−1 towards the end of the bloom. Important accessory pigments were peridinin (indicative of dinophytes) and fucoxanthin (diatoms). Stepwise multiple regression showed that peridinin was the best predictor of chl a. For the first time, in situ evidence for the mediation of (wave) ripple migration by microalgae is provided. Results indicate that diatoms, and quite possibly dinophytes, can have a significant effect on intertidal flat ripple mobility on a temporal scale of weeks. In addition, microalgal effects appear capable of effecting a reduction in bed roughness on a spatial scale of up to 10−2 m, with a subsequent reduction in bottom stress and bed erodability. It is suggested that a unique combination of environmental conditions, in conjunction with the microalgal bloom(s), promoted the initial cessation of ripple movement, and that stationary-phase, diatom-derived extracellular polymeric substances (EPS) (and possibly dinophyte-derived EPS) may have prolonged the condition. It is reasonable to suppose that ripple stabilisation by similar processes may have contributed to ripple mark preservation in the geological record. A conceptual model of sandy intertidal flat processes is presented, illustrating two conditions: (i) a low EPS/microalgae sediment content with low ripple stabilisation and preservation potential; and (ii) a high EPS/microalgae content with higher preservation potential.