Organic-walled dinoflagellate cyst assemblages were analysed in 31 surface sediment samples from the Ría de Vigo (NW Iberia) to obtain supporting evidence for the interpretation of past environmental signals from sediment cores. Complementarily, the totals of pollen (and pollen from riparian taxa), foraminiferal linings and freshwater algae were also considered to test their value as (palaeo)environmental indicators in fluvio-marine sedimentary environments. Abundances of foraminiferal linings gradually increased towards the ría's mouth, which supports its use as a proxy to infer the degree of marine influence in the sediment record. The ratio of dinoflagellate cysts to pollen and spores (D/P) increased with distance to the main river's mouth (and water depth) in the inner (<7 m water depth) and the outer (>20 m) parts of the ría. Total pollen concentrations decreased with water depth in the outer part but did not show any clear trend in the rest of the ría. No clear pattern in the distributions of pollen from riparian plants and spores from freshwater microalgae was detected. Multivariate analyses (clustering and RDA) performed on dinoflagellate cyst records and environmental data reflected a marked inshore-offshore distribution pattern mainly controlled by a fluvio-marine environmental gradient. Increasing abundances of cysts of Gymnodinium species and heterotrophic cysts as well as higher cyst diversity characterised the deeper environments of the outer ría. These observations suggest a relationship with increased shelf influence and are compatible with the heterotroph upwelling signal described in previous works. A very different cyst association with a predominance of autotrophic cysts characterised the intermediate and inner parts of ría, where exceptionally high cyst abundances of Lingulodinium polyedra (~56–99% and ~ 200–114,000 cysts.g−1) were reported. Abundances of cysts of L. polyedra positively correlated with shallower and higher river-influenced environments characterised by higher sea-surface temperature. Our results agree with previous studies and reinforce the value of this species as an indicator of warmer and stratified conditions. Moreover, cysts of L. polyedra positively correlated with winter sea-surface nitrate contents, which is compatible with the nutrient enrichment signal (natural or anthropogenic) that has already been described in other deep and stratified estuarine environments and is consistent with historical cyst records obtained in the Ría de Vigo. However, further research is needed to disentangle the nutrient enrichment signal from the influence of other environmental factors.