Heat the olive oil in a medium saucepan over medium-high heat. Add the onion, bell pepper, and jalapeño and season with salt and black pepper, to taste. Cook for 4-5 minutes, stirring occasionally until the onion and peppers become soft.
Add the tomatoes, oregano, smoked paprika, crushed red pepper flakes, and water. Stir to combine and reduce the heat to medium-low. Continue cooking, stirring occasionally, for another 4-5 minutes.
Remove from the heat and set aside to cool for a few minutes. Once slightly cool, pureé the mixture with an immersion blender, leaving slightly chunky, or transfer to a regular blender or food processor and pulse a couple of times until just blended.
Transfer the salsa to a bowl and stir in fresh lime juice and cilantro.
Season with additional salt and black pepper, if desired.
Serve immediately or cover and place in the refrigerator until ready to use as a dip with tortilla chips or as a side with Mexican or Tex-Mex entreés. Enjoy!