SAN YSIDRO, Calif. — Assaults against U.S. Border Patrol agents nearly doubled along the Mexican border over the last year as patrols cracking down on drug trafficking and migrant smuggling encountered increasing resistance — including the use of rocks, Molotov cocktails and gunfire. At least 687 assaults against agents were reported during the fiscal year that ended Sept. 30, up from the previous year's total of 354 and the highest since the agency began tracking assaults across the Southwest border in the late 1990s, according to Border Patrol officials. Most assaults occurred near urban smuggling havens such as Nogales, Ariz., and Tijuana, but cross-border skirmishes took place from remote California deserts to the banks of the Rio Grande in Texas. In many attacks, smugglers hurled softball-size rocks or fired high-powered slingshot devices loaded with marbles and ball bearings. Some tried to run over agents with vehicles. In some cases, smugglers and migrants fought with agents and tossed wooden pallets to block their pursuers. Dented and damaged vehicles, windshields shattered, sat in Border Patrol parking lots. In Tucson and San Diego, the most violent sectors, agents reported being shot at 43 times — up from 18 the previous year. No agents were killed, but three were shot in the leg. At least 20 more were hospitalized, many with head injuries from rocks. Agents fatally shot five suspected smugglers in the Tucson and San Diego sectors. In one recent case, officials said, an agent struggled with and killed a man who was armed with a semiautomatic weapon and was suspected of waiting to pick up migrants. Officials attribute the increased number of assaults to rising frustration among drug and immigrant traffickers, who have seen traditional smuggling routes blocked by the border buildup. About 11,000 agents — more than ever — patrol the 2,000-mile border with Mexico. Stadium lighting, sensors, remote cameras and triple fences protect some frontiers. "They're feeling they have to fight their way through now," said Agent Jim Hawkins, a spokesman for the agency's Tucson sector. "We're taking their livelihood away from them, so they're getting angry and desperate." On one stretch of border near San Diego, rock-throwing and other violent acts have become so common that officials plan to erect signs warning that assaulting agents is against the law. The recent surge, officials say, doesn't match the level and intensity of violence in San Diego County in the early to mid-1990s, when agents wore riot gear and formed special units to disperse crowds of migrants and to combat widespread banditry. The recent violence has spread out across the Southwest as illegal immigration corridors have shifted. Most assaults occur in Arizona and California, where borders have been heavily fortified. Agents and experts expect the hostile climate to intensify as the border becomes increasingly difficult to cross. "It's a combustible mixture," said Wayne Cornelius, director of the Center for Comparative Immigration Studies at UC San Diego. "It's inevitable there will be an escalation of violence on both sides, because the traffic hasn't diminished … and the desperation of those trying to get in is just as great as it has ever been." While immigrant smugglers mostly throw rocks to distract agents, drug traffickers are more likely to use weapons and committed the most serious assaults in the past year, officials say. In June, two agents following a rural smuggling trail east of Nogales fought a fierce gun battle with several suspected drug runners. Both agents suffered leg wounds but kept returning fire, officials said. The suspects fled back to Mexico. In another clash, an agent patrolling a rugged area east of San Diego over the summer came under a hail of gunfire as he approached a vehicle being loaded with drugs. More than 23 bullets, believed to have been fired from Mexico, hit the agent's vehicle. He suffered a minor leg wound. Most assaults occur along highly fortified border areas across from hillside urban shantytowns. Smugglers throw rocks or fire slingshots or paintballs at agents from the higher vantage points. They flee when Mexican authorities arrive or when agents fire back with launchers that shoot exploding balls filled with pepper spray. Agents say Border Patrol measures are often countered with more aggressive tactics from the smugglers. "It's just a matter of time before they start shooting at us. We're making it too hard for them," said Matilde Torres, a supervisory agent who works a rock-strewn, nine-mile stretch across from Tijuana's notorious Colonia Libertad neighborhood. After agents began using pepper ball launchers a few years ago, smugglers countered with slingshots. Agents in turn began aiming the launchers at torsos instead of feet. Torres, standing about 50 feet north of the border fence, pointed to ramshackle buildings in Tijuana that bore the marks of dozens of bursts from pepper spray rounds. Assaults launched from atop the border fence draw return fire from agents, he said. "That fence belongs to the U.S.," he said. "If they are on it, we will engage them." Torres said smugglers often try to cross the border here because once they climb over the two border fences, it's only a short sprint to San Ysidro, a quick taxi or trolley ride away from downtown San Diego. "If this was midnight, I couldn't park my vehicle here without being rocked," Torres said. Above him dangled a remote camera that was knocked down, most likely by smugglers, shortly after being erected earlier this year. To avoid being struck by flying objects, Torres said the Border Patrol now planned to cut gun portholes in the second border fence so they could fire pepper ball rounds at smugglers without being exposed. In other dangerous areas, agents drive customized rock-proof vehicles, dubbed war wagons for their armored exterior. Some of the windows are bulletproof. The vehicles, in use for years, are needed more than ever, officials said, especially in Nogales and in Calexico, Calif., across the border from Mexicali, where smugglers in recent months have started tossing Molotov cocktails at agents. In one recent case, a person on the border fence threw a Molotov cocktail atop the roof of a vehicle. "We got lucky…. It failed to ignite," said Lloyd Frers, a Border Patrol spokesman. Border Patrol officials near San Diego, hoping to curb the violence, are planning to add 40 remote cameras and 13 blue alert lights atop existing towers to help guide Mexican authorities to problem areas. Their Mexican counterparts have agreed to erect 50 signs along the fence warning people that assaulting agents is against the law. Joe Perez, patrol agent in charge of the busy Chula Vista sector near San Diego, said tensions were near a "boiling point" and expected many of the signs to be torn down. Still, he said the smugglers would be put on notice that there were serious consequences. "It's one way of getting the word out," Perez said.