This study evaluated the influence of human disturbance in nesting success of little tern (Sterna albifrons) and its interaction with the intrinsic seasonal variation in the birds’ breeding biology. During 2003–2005 we studied little tern nesting ecology in southern Portugal in two different types of habitat: their natural habitat (sandy beaches) and a man-made habitat (salinas). In both habitat types, annual variations were found in the distribution of nest initiation over the breeding season and in the size of the clutches. The percentage of nests producing hatched chicks varied between 26.7% and 66.4% in different years and habitats. The main causes of hatching failure varied between years and habitats, but predation, flooding and human activities were very common. No consistent differences in breeding parameters or nesting success were found between habitats. On sandy beaches, the effect of protective measures (warning signs and wardening) on nesting success, together with differences between years and within each breeding season, were assessed using a logistic regression model. The presence/absence of protective measures was the most important predictor of nesting success, with birds being up to 34 times more likely to succeed with protective measures. Seasonal declines were found for clutch size and egg volume, and season was also an important predictor of nesting success, with nests more likely to succeed earlier in the season. Hence, earlier breeders will be those that benefit more from protective measures, suggesting that conservation efforts for little tern can be maximised if concentrated earlier in the season.