The most straightforward method of increasing a low CR creature’s CR is by giving it class levels or by increasing it’s stats using the table in the back of the DMG. It’s a bit tedious, but it makes a more interesting creature once you are finished with it. No one expects the goblin with wizard levels or the kuo-toa with levels in monk!
More of them
Don’t do this one often, but you can always send a large number of low-CR monsters at the party. While adding class levels requires a lot of prep time, lots of monsters requires a lot of wasted in-game time, and that has potential to bore the players. But every once in a while, you can just send a whole bunch of monsters at them. When it doesn’t happen every single session, it’s a fun romp for the players to be able to feel powerful but still run the real risk of damage. Thanks to 5e’s bounded accuracy, more enemy attacks means more potential harm.
When players realize that the normally low-level encounter they are facing offers a lasting debuff attached to it, suddenly the encounter becomes more meaningful. They will have to take extra steps to avoid diseases, poisons, magical effects, or injury. For instance, a regular old giant rat is no threat at all at a pathetic CR of 1/8. But the locals have all been suffering from a plague carried by vermin, suddenly a bunch of rats has potential of ruining a PC’s entire day if they fail a save. Melee characters might opt to fight from range or spellcasters might need to burn a higher-than-normal spell slot to take them out quickly. A drow that drops a large creature with a small cut before going after the PCs suddenly becomes a hit away from poisoning a PC with who knows what sort of diabolical substance.
Environmental hazards can make advantages for enemies and disadvantages for the party which together can significantly alter an encounter’s CR. If kobolds are firing crossbows prone from high ground and have cover firing upon the PCs in an open area with plenty of traps hidden all over and a lava moat to find a way across, the PCs will take plenty of damage before ever reaching them. Even if they don’t take damage, they will likely waste valuable resources over a handful of kobolds. Carefully tailor your encounters in the enemies’ favor if they are a lower CR than the players, who will have to get lucky or clever to overcome the tipped scales.
There’s always a handful of abilities that you can throw at the PCs. Whether it’s the ones in the book (shoving, grappling, flanking) or ones you invent as a DM. Matt Colville once defending 4e D&D and its Powers for enemies. They always did something, and in terms of monsters they were occasionally unique to other editions of D&D. Try adding some unique abilities to your lower-level monsters that make sense for that creature. When I ran a game with an Aboleth, I heavily homebrewed some new abilities for it to surprise my players. I gave it a sort of Mind Blast (like a Mind Flayer) that would only knock creatures unconscious, making it easier to capture and enthrall players that got separated. I also gave it the ability to phase through ice as it was in a giant “aquarium” with ice walls, so it could either observe the PCs from its murky water or attack when it chose to reveal itself, or even drag a PC into the tank with it to coat it in its diseased mucous. Admittedly, an Aboleth is not a low-CR monster. But on its own, the PCs would have easily taken it out so I gave this guy plenty of advantages to tip the odds in its favor and the players still pulled through eventually. But I had made an easy encounter into a very challenging one.
Increasing the stakes of an encounter can alter how PCs approach a challenge. If players have to stay undetected, then even a bunch of orcs will be a threat to a party trying to sneak by a low-level monster, because it’s no longer about “can they kill it?” but “can they kill it before it has a chance to yell or else sneak by it?” Another option might be a requirement NOT to kill the creatures in an area. Maybe they are breaking into their own allies’ palace for information or to ‘borrow’ some magic item, but have no ill intent against the guards. Killing one might put them at massive fault. A time limit can increase the stakes of an encounter where they actually need to consider “should we waste time to kill these low-level creatures?” Perhaps those low-level creatures need to just be avoided instead so the players don’t spend too many precious rounds dealing with combat. There are plenty of other ways to increase the stakes of a battle, so get creative!