Slice the cucumbers into 1/4-inch rounds and the red onion into thin half-moons. Layer the cucumbers, onion, and fresh dill into a clean jar, distributing them evenly. This helps ensure even flavor distribution throughout the pickles as the brine infuses.
Sprinkle the kosher salt and freshly ground black pepper evenly over the layered vegetables in the jar. I like to season in two additions—once after the first half of vegetables and once after layering everything—so the salt can start drawing out the cucumber's moisture for better texture and flavor absorption.
In a separate bowl or measuring cup, whisk together the filtered water, apple cider vinegar, granulated sugar, and whole mustard seeds until the sugar dissolves completely. Pour this brine over the vegetables in the jar until they are fully submerged—submerging is crucial to prevent spoilage and ensure even pickling. I find that pressing down gently on the vegetables helps keep them under the liquid.
Close the jar tightly and place it in the refrigerator for at least 30 minutes before eating, though the pickles will continue to develop deeper flavor over the next 24-48 hours. These refrigerator pickles keep for up to 2 weeks and are best enjoyed within the first week when the cucumbers maintain their crispness.