as you can see in the image, the cube’s “shadow” overrides the reflection of objects behind it. Is this simply the limitation of SSR or can it be fixed?
It’s expected.
SSR retrieve what’s on screen and use it to create a “fake” reflection.
As you can see on your image, the cube blocks the view and we can’t see the middle of the tree behind so this is why there’s a “hole” in the reflection below since the system cannot invent what’s behind the cube so it fallback on the sky cubemap
However, SSR is supposed to be used in combination with reflection probe. If you place and bake a probe, the SSR system will first fallback on the reflection probe to see if it has information about the missing piece, this might help fix your missing middle part of the tree 
Cheers.
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Thank you for the answer; I used the light probe with the HDRP water object and also an alternative water material but still gave mixed results (sometimes only barely works at a certain distance/angle). How should I go about placing the reflection probe on the lake? Should there be multiple?
You should make sure there’s a main reflection probe capture the full tree. And then depending on the result and where your player (camera) can go, you can carefully place multiples to fill some gaps. Keep in mind that depending on the projection (the shape and size) of the reflections probes, the result will be different.
When the checkbox called “Use influence volume as Proxy volume”, the reflection probe actual shape and size will be used to project its results on reflective surface so this will affect how the result look.