Возможное решение с основанием R будет:
d <- data.frame(station = rep(paste("station", 1:3), c(250, 1000, 150)),
depth = rnorm(250 + 1000 + 150, 100, 10))
d$grp_counter <- do.call("c", lapply(tapply(d$depth, d$station, length), seq_len))
d$grp_length <- rep(tapply(d$depth, d$station, length), tapply(d$depth, d$station, length))
d <- d[d$grp_counter <= (d$grp_length - 50),]
d
# OR w/o auxiliary vars: subset(d, select = -c(grp_counter, grp_length))