You are asking a question that none of us can fully answer.
First, rain or washing is not going to cause toxic substances to leech out (if any are present to begin with) like being submerged will; the same holds for wood. Once these items are permanently under water, the water will penetrate the rock or wood, depending (in the case of rock) upon the composition as some rock is more porous than other rock. Granite is fairly dense, but I'm not a geologist so I can't say to what extent. As the water penetrates the rock, it can pick up toxic substances and draw them out, so to speak.
But again, without knowing the total history of the rock in question, we have no way of knowing what if any substances it may have absorbed over its history exposed in the yard.
Water changes are not always sufficient to dilute such toxins, depending what they are and in what strength. Let me give you a personal example of the problem I had from a piece of wood. I bought it in a fish store, so I expected it was OK. I had a lot of wood in my 115g tank. After several months, during which I did 50% water changes weekly (I still do this), I noticed the fish were getting lethargic, esp the Corydoras [they are highly susceptible to toxins and frequently are the first to show signs of something being wrong]; they sat on leaves respirating very heavily but slowly. New fish put into the tank died within a couple days. I tested for everything imaginable, nothing. Finally I was referred to the Freshwater Fishes Curator at the Vancouver Aquarium, and we started exploring possible causes. The second cause he considered was something toxic in the wood. I removed all of it, did a 75% water change, and the response from the fish was amazing. By the end of a week though they began to show symptoms again. He surmised that whatever was in one (or more) pieces of the wood had probably slowly leeched into the tank and adhered to the gravel, plant leaves, filter media, rocks, etc. I pulled the tank completely apart, washed the gravel in buckets of very hot water, washed the plant leaves, replaced the filter media, scrubbed the rocks. Put it all back together, and no problems thereafter. Something toxic in the wood had obviously slowly leeched out and been absorbed elsewhere. It can take years for this to manifest itself. It is now some 15 years after that catastrophe, I have the same gravel and the same rocks, all new wood; it has never returned.