Based on the rules I have read on Call of Cthulhu it seems like drowning in this game is very easy. The skill used to avoid drowning rarely has points put into it. How can I make water less lethal even in cases where there is dangerous water?
They'll only drown if you let them, Keeper.
Swimming to safety (drowning):
An investigator has fallen into turbulent water and must swim to safety or drown. The Keeper calls for a swim roll with the goal "swim to safety." If the player loses, then no progress is made and water may be inhaled; the player must make a CON roll or his or her investigator will suffer 1D6 damage per round (see Other Forms of Damage, page 124). The situation demands a pushed roll—the only alternative is that the investigator gives up and drowns. If the player misses the pushed swim roll, the investigator is battered and half-drowned, taking 1D6 damage per round. The Keeper must then make an important decision: either the investigator’s life is put on the line or the investigator is washed up later elsewhere. If the Keeper chooses the former, then the investigator will continue to lose hit points each round until saved by another investigator or non-player character. Alternatively, if no one else is around, the Keeper could waive the drowning damage and instead have the unsuccessful pushed roll mean that the investigator has washed up on some foreign shore, bereft of all possessions and in a bad way.
-- "A Guide to Using the Rules for Specific Situations", CoC7e Keeper Rulebook p.204
Of course, to start with:
Only roll Swim in times of crisis or danger, or when the Keeper judges it appropriate. [...] Swimming a length in the swimming pool: no roll required
-- "Skill List", CoC7e Keeper Rulebook p. 77
You're the one who decides if there's enough crisis or danger to call for a swim roll. You're the one who decides what happens when a swim roll (or a pushed swim roll) fails, because the roll is not about the simple success or failure of swimming but about whether the investigators accomplish their goal or not.
If an investigator is attempting to swim away from some aquatic or semi-aquatic pursuers, an easy potential alternative is to just have them be captured -- at least, if that capture would wind up less dangerous than drowning, in the short term.
If an investigator falls off a riverboat during a pitched fight but in otherwise calm water, the Swim objective might just be to get themselves back on the boat, and a failed roll doesn't so much get them somehow sucked to the bottom of the river as leave them tapped out and unable to get back up on the boat unless another investigator helps.
If you want the dice to decide, you can let the dice decide.
Now, just as a preface, while I understand a desire to not want to feel like you're personally responsible for deciding whether a PC lives or dies, even in the most random-looking of cases you're still the one who made water a hazard in the first place, knowing how bad your investigators are at swimming, and you're the one who decided that it should come into play.
If, knowing all that, you're still of two minds about whether circumstances are going to turn lethal or not, you can always turn to the same dice that decide whether or not somebody dies from, say, a car crash or a gunshot: the damage dice.
So here's that Other Forms of Damage table for the rules if it does come to drowning:
Asphyxiation and Drowning: a CON roll should be made each round; once a CON roll is failed, damage is sustained each round thereafter until death or until the victim is able to breathe. If the character is in a state of physical exertion, a Hard success is required on the CON roll. Death occurs at 0 hit points (ignore the Major Wound rule).
-- "Other Forms of Damage", CoC7e Keeper Rulebook p.124
Like the "swimming to safety" setup tells you, when someone fails a Swim roll in drown conditions, they have a choice - they can push the roll and start drowning immediately if it fails, or give up on all attempts to save themselves and start making CON rolls to avoid drowning.
The example assumes a single abandoned investigator, but if you're in a situation where other investigators can provide help, you can just start ticking off the CON checks or drown damage round by round and see if the investigator survives.
If you're not in a situation where other investigators can provide help, it gets a little more complicated. Decide the total drowning damage somebody will take before they're somehow washed to safety, as a number of d6s. When gauging lethality, note that 3d6 about lines up with 2d10 and 6d6 with 4d10, and you may even want to go higher than that. When you offer the chance to push the Swim roll, you can lay out the alternatives - push and take all the drowning damage on a failure, or make CON checks until they fail (with exertion as appropriate), taking 1d6 less damage with every success. Regardless of what you end up rolling it's still all drowning damage taken over time - it won't cause a Major Wound (well, maybe if someone has only 12 hit points and you get lucky) but you don't need an investigator to take a Major Wound to die when their HP hits 0.
Note the guidance on rolls.
Here are some examples of goals and how a Keeper might use the rules to resolve them. These are not spot rules and are only provided as suggestions to help Keepers understand how skill rolls can be used with a variety of goals.
"A Guide to Using the Rules for Specific Situations", CoC7e Keeper Rulebook p.204
You can make up rules as you wish to handle drowning.
Anyway, I would only apply drowning rules so long as some sort of entity, be it turbulent water or a monster is attempting to drown them. If they handle the monster through evasion or violence, they can swim away freely. They can help their companions who lack such skills and fail swimming rolls.
What I would do is have an initial confrontation where whatever problematic monster was coming, wherein they could resolve the conflict with or without rolls or get bonus dice, then a direct one on one confrontation between a person or people and whatever threat, one where they can creatively use skills which are better than swimming to resolve that problem, and then swimming rolls.
That gives them three chances to roll or roleplay well to resolve the problem or mitigate it. You could reduce that for a greater threat, of course.
Once they get into a drowning situation you can adjust the damage as necessary, as they jerk up and down in the water. This is a good chance to lay on the horror of the deep and the foolishness of mortals treading in land where they shouldn't have gone. Then they or their companions can resolve the threat, or be drowned or dragged to an underwater lair depending on the stakes.