Line a 9x9 pan with parchment paper and scatter coarsely chopped almonds evenly over the bottom. Set aside.
Combine butter, sugar, water, and salt in a medium-sized pot over medium heat. Meanwhile measure out your vanilla extract and have it ready nearby.
Stir ingredients frequently over medium heat. During this time (only before boiling), use a wet pastry brush to brush down the sides where any sugar may settle on the side of the pot to prevent sugar crystals. Continue to stir frequently until mixture comes to a boil (this may take a while, have patience and do not turn up the heat or you will ruin your toffee).
Once the mixture comes to a boil, attach your candy thermometer. Make sure that the point of the candy thermometer is not touching the bottom of your pan.
Continue to stir occasionally, the mixture will slowly thicken and will turn a more yellow hue as it cooks, and cook to hard crack (305°F/151°C).
Once toffee reaches 305°F/151°C, immediately remove from heat and stir in vanilla extract (careful, it bubbles and steams a bit).
Pour mixture evenly into your prepared pan over the almonds. Allow to sit for 5 minutes and then sprinkle chocolate chips evenly overtop the mixture. Cover with foil and allow to sit another 5 minutes, then remove the foil and use a spatula to gently spread chocolate chips evenly over your toffee.
Immediately sprinkle with additional finely chopped almonds and flaky sea salt, if desired. Allow to cool completely at room temperature before breaking and serving.