"Changes in" , "Changes of" or "Changes to"

I should say I have no idea about both "Geographic Science" and "intended meaning". So I will answer pointing out possible "senses" that those prepositions contribute to the sentence when used together with "change".

In: shows a state, condition, character, or quality. E.g. change in attitudes

of: implies some sort of "replacement". E.g. change of government

from, to: implies transition / transformation. E.g. a color change from green to brown

Here are the implications as per my understanding:

1. Changes in wetland hydrological and landscape variables can alter the population dynamics of waterbirds.

The implication is some kind of chemical or similar changes that have been observed in the midlands. These are not conscious or active alterations but could be due to a larger phenomenon or some kind of pollution or similar.

2. Changes of hydrology and landscapes in wetlands can alter the population dynamics of waterbirds.

The implication is of replacement such as replacing one kind of hydrology or landscape with another.

3. Changes to hydrology and landscapes in wetlands can alter the population dynamics of waterbirds.

There is the implication of an outer hand that is making these changes or alterations and the tone is somewhat of a warning.

4. Hydrological and landscape changes in wetlands can alter the population dynamics of waterbirds.

In this sentence formation the emphasis is on Hydrological and landscape change with the exclusion of other changes.

Hope it helps