Simulating datasets of species abundances with varying degrees of turnover in R
Without any example of your data or distributions it is a hard question to answer. Without further info I think there are two approaches:


resample your data using stratified sampling. The R sample package can be of good help here.
generate a multivariate distribution, as far as I know there are no packages that will directly do this for you. Depending on the distributions of your data, creating the right multivariate distribution which includes the right correlations may be very hard. In some cases you may even need to use copulas (this is especially necessary if you are interested in tail events, correlation will not be sufficient to create dependence of these events). Note that this topic can be a separate PhD thesis on itself.


I hope this helps.