‘Can’t’ is really too passive to use if it really is ‘must not’ for anything serious, so while the sentence could work either way in spoken communication (because you can convey enough context with tone of voice and emphasis to imply which sense you mean), it would still not be a great choice of words if you mean the second sense.
In this case a negative imperative is what you should be using. Moreover, since it's a life-or-death matter, we need to carefully explain ourselves. "Do not add too much water to the reactor. If you add too much water, the reactor could explode. The reactor should never contain more than 1000 litres of water. If it is overfilled, immediately follow the steps in 3.4.1 to perform an emergency evacuation." By being careful in our follow up, we reduce the risk of any misunderstanding. We cannot prevent a person from misunderstanding, but at least they are more likely to realise they have misunderstood something and seek clarification.
"Must not" is reasonably well-understood by native speakers of English, but it is confusing to non-native speakers because even though "must"="have to", the negations have different meanings. It is no use being technically correct if the person whose responsibility it is thinks you said "you don't have to add too much water to the reactor". The prevalence of "must" also varies throughout the native-speaking world.