One of the problems that plagued older rechargeable batteries (e.g. Nickel Cadmium ($\text{NiCad}$) and Nickel Metal Hydride ($\text{NiMH}$)) was the memory effect. The memory effect occurs when a rechargeable battery is not fully discharged. It then "forgets" that it has a greater capacity than it thinks it has, and so in the future it discharges less.
A good example is a water bottle. Initially, water bottles have a certain capacity for water. Let's say that I drink most of the water in a water bottle during one usage. If the memory effect affected water bottles, I would not be able to drink any water in the future occupying the space that had held the water that had not been drunken the last time. That extra space would be forever lost. Over time, this can wear down a rechargeable battery. Fortunately, this generally only affects $\text{NiCad}$ and $\text{NiMH}$ rechargeable batteries.
I haven't been able to find much about effects that influence only lithium ion batteries, but there are a lot of across-the-board factors. Here's a short list:
- Chemicals breaking down
- Passivation (which affects lithium ion batteries), which is when a layer of unwanted chemicals form on the battery cell. This discusses a related phenomenon on page 4258:
Unfortunately, on recharge, the lithium has a strong tendency to form mossy deposits and dendrites in the usual liquid organic solvents (cf. Figure 15B). This limits the cycle life to 100-150 cycles (considerably lower that the 300 cycles required for a commercial cell), as well as increasing the risk of a safety incident.
- Mechanical stresses and leaking. Batteries can be damaged in a variety of ways, causing internal components to break and causing chemicals to leak out. This can be very dangerous to humans.
There are other long-term factors that increase battery aging. The page I linked for the above list seems to be fond of the
Arrhenius equation:
$$k=Ae^{-E_a/RT}$$
which shows that the rate of chemical reations changes as temperature changes. High temperatures mean faster reactions but also possibly a shorter life; this can affect non-rechargeable batteries significantly.
Finally, there's the phenomenon of self-discharge, which is when unwanted reactions in the battery "eat away," so to speak, at the battery's capacity. The process can differ based on the type of battery. Battery University has a page on it, which you may have already seen. It reiterates that temperature can speed up this process. Scarily enough, lithium ion batteries may discharge as much as 5% within the first 24 hours, slowing down to 1-2% per month after that.