Encounters Based on Ecology & Behavior?

[Palanan]

One of my players has a background in outdoorsy things and is currently playing a druid, and for our next session I’d like to run an encounter that’s less about combat and more about unraveling some sort of small ecological mystery.

Are there any encounters like this in any published books or modules? And if not, can anyone help me come up with something? I’m looking for something that could be played through in 1-2 short sessions, which will let my druid player draw on some of his real-life interests to solve an in-game challenge. I'm running Pathfinder, but I'm open to ideas and scenarios from any edition.

Anything come to mind? And how could I go about designing something like this?

[Vahnavoi]

You're better off watching nature documentaries for inspiration than anything already existing on the tabletop.

Actual ecological mysteries that occur:

Why did our crops fail despite being plentiful for years? (Answer: the soil was depleted or a new kind of disease emerged to which mono-plant agriculture is particularly vulnerable.)
Why are pests staying away from my neighbor's field, but not mine? (Answer: because some plant they're growing is a natural pest repellent or because some unseen predator has migrated nearby)
Why has a previously plentiful game creature all but vanished? (Answer: over-hunting or a new disease)
Why is there suddenly too many of once harmless game creature? (Answer: its chief predator was over-hunted or food supply has suddenly increased, leading to population boom.)
Why did all the farm animals suddenly grow nervous and bolt? (Answer: possible predictor of an earthquake, a tsunami or some other natural disaster.)
Why does some swarm of creatures appear like clockwork every few years?
Where do these migrating beasts go when they're not here?
Where do these things come from? How do they reproduce?
Why are several different species suddenly becoming weaker or dying? (Answer: deep or widespread disturbance in the entire food chain, such as dearth of a vital mineral.)
Why does this creature do this really weird thing? (Answer: for sex and reproduction, until we find otherwise)
Is this creature intelligent or am I just imagining things? (Answer: yes to both; it's intelligent but not in the exact way you are.)

[KorvinStarmast]

Why are there suddenly many more deer than usual in this area, and why are they migrating to the (north/south/east/west), and why are a lot of other forest creatures moving in the same direction.

Answer: a new apex predator arrived recently (a green or black dragon) (How does one deal with a dragon, eh?)

Answer: a recent forest fire (Who started it?)

[Khedrac]

Why does some swarm of creatures appear like clockwork every few years?

Vahnavoi's suggestion of watching nature documentaries is excellent, but I thought this example worth expanding upon - you might get better results ignoring the word "few"!
In north-east India (the bit between east of Bangladesh) roughly every 50 years they get a massive rat horde swarming out of the forests and eating everything they can. With a 50-year interval it is long enough to both get forgotten and not have the details properly recorded to make it predictable. However because it is localised - some areas will get it one year, others will get it the next - last time round some researchers were able to do the analysis, consult the records and work out what was going on. The bamboo forests flower and fruit every 50 years - and the rats emerge roughly 9 months later. (They go into a rapid breeding cycle until the fruit is exhausted and then leave the forests looking for food.)
In a fantasy world the elves and other long-lived races will be the ones to realise that this is cyclical (and the ones to go to for answers) but the shorter-lived races are likely to be taken unaware.